A True War Story
by Onyx Productions
Summary: Mass Effect AU where Tali and Shepard are best friends and meet before the events of ME. Will lead all the way through to ME3. Sorry for the short summery. M for violence, language, and sexual scenes later on. Also considering Garrus/Liara and OC/Kasumi. Oh yea, OC! Will appear soon! -On hold so I can work my other stories-
1. A Beautiful Friendship

**OK so I want to take on a Mass Effect AU where Shepard and Tali met BEFORE the events of Mass Effect 1 and actually before Shepard became Commander Shepard. I got the inspiration from Mega-Moto and his story Mass Effect: A Different Path. I want to create my own ShepxTali story but I want it to be a dark and gritty universe. That being said, there are a few minor changes to the lore. The only major thing that has been changed is Shepard's background (I mean origin story) and the Council has a Batarian Councilor, which is going to play a major part later on. It will run from ME all the way through to ME3. It will include The fallowing DLC: The Arrival, Cerberus Network (Zaeed), Kasumi: Stolen Money, From Ashes, Leviathan, and Citadel. The ending will also be altered slightly just to please those who are unhappy with it. Anyways, I think I have rambled on long enough. Let us begin our adventure into a new Mass Effect!**

* * *

**Mass Effect  
A True War Story**

* * *

**Chapter 1  
A Beautiful Friendship**

* * *

It was dark. The only light was that of the stars above. The young boy, not older than eight, laid on his bed looking up; he couldn't help but think of the many planets and systems that were out there. His door opened and he turned. A tall woman with short red hair approached. She wore a navy uniform, a commander uniform. "I came to say good-night," she said tenderly as she sat at the end of bed. She reached over and neatly tucked the boy in. Her blue eyes filled with love and compassion. "_Stargazing _I see," she said as she looked up at the stars. The boy lay silently, as if he had to look or else the stars would disappear. The women chuckled. "Just like me. Looking at the stars, dreaming of the many species of life," she said with a whisper and wide smile.

"When can I go to the stars mom?" the boy asked, eyes still glued to the stars.

"I promise you that one of these days, you will go there," she said. She leaned in and kissed boy on the forehead. "I promise you John, one of these days you will go there and change everything. You know why?" she asked the young boy.

He finally looked at her, his bright green eyes filled with curiosity. "Why?"

"Because you are a Shepard; and that means that you can do anything if you have the will to do it," she said as she kissed him again. "Now get some sleep, tomorrow is a big day for you," she said. His curiosity rose even more.

Before she could leave the room, John stopped her at the door. "Why?"

She turned just slightly, enough to only see over her shoulder, "It's a surprise."

* * *

John Shepard was born on Earth on April 11th, 2154. He grew a good life. His mom was Commander Jennifer Shepard, a decorated Alliance soldier who was nominated for the N7 program. He lived with his father, James, and his two sisters Jasmine and Elli in the countryside, just outside of Salem Organ. His father worked for a local gun store and John was typically left to raise his sisters. He was responsible. He had to be. His father wasn't strict, but he knew that John would accomplish a lot; only if he was responsible however. John was a stargazer; all he wanted to do was explore the galaxy, to see the different forms of life and to learn the many cultures. When he was eight years old he got his wish. His mother allowed him to see the planet Eden Prime, where he and his family would now live. The sudden move made John the happiest kid in the galaxy.

* * *

Eden Prime was a beautiful world. No, beautiful couldn't even describe it. John was standing in his backyard. They owned thirty acres of land, and his backyard was a forest, literally. His father had put up a fence, so that he knew when it was time to turn back. Although his father trusted him, his mother didn't; hiding numerous cameras all around so she could easily catch him fast if he left the perimeter. He was just sitting there just looking at the forest. At the edge of his vision, he noticed his youngest sister, Elli, sneaking up on him. She lunged, simultaneously yelling "Your it!" Even though John was able to quickly back away, she still tagged him, barley.

He laughed, "Ok, your going down!" he yelled playfully. He began to chase her into the forest. They were laughing and running. John lost sight of her. He studied the area. He looked at the ground to find tracks. He fallowed them to a tree. She was hiding on the other side of it, unaware of him. He knelt down and quietly approached. He was close, he could taste victory. Suddenly, as if he was a rag doll, he was thrown into the air. He flew back several feet. He was dizzy, unaware of what had happened. All he could feel was heat. He could hear only a high pitched noise, like an alarm. He was blinded by a bright red light. A fire! He quickly sat up and realized that the forest was on fire. He started back towards his house then stopped, dead in his tracks, "Elli!" he said aloud. He sprinted back towards the fire. The tress was ablaze and smoke filled the air. He held his arm up to protect his eyes and mouth from the smoke. A searched the area he last saw Elli in and began to call her name.

"ELLI!" No reply.

"ELLI, COME ON I KNOW YOU'RE HERE!" Once again there was no reply.

"PLEASE ELLI!" This time there was a reply but not from Elli, from someone else.

"Don't worry, she's ok, but you won't be!" The voice was raspy and deep. John turned to the origin of the voice and was greeted by a shotgun bud to the face. He was unconscious.

* * *

He woke up to see nothing but blackness. He tried to move but his hands were bound. HE quickly realized that he was blindfolded, gagged, and tied. He was smart though. He still had ears after all. He could hear several men arguing, based on the pitch of the voices, they were several feet away, obviously trying to keep their voices down for him not to hear. "I say we waste the kid, he aint got nothing to give us," said the first voice. John knew the only ones sick enough to kidnap a child of his age was the Vorcha. He read a lot growing up, to prepare himself for the potential dangers of the galaxy, he knew the Vorcha were sick sadistic creatures.

He suddenly heard a new voice, a female one. "Now just hold on, in case you hadn't noticed, he is obviously rich due to the landscape. Bribe the parents and get a few million, then we waste him," she said cynically.

"Fuck him and his sister, we sell her and we waste him!" said a third voice, the same voice he heard before he was knocked out. John quickly realized that this was a well organized attack. He tried to think of a way out. Suddenly, an idea popped into his head. One that could work but was highly stupid and had a high chance of getting him killed then free. John began to scream and yell, it being muffled by the gag but it was loud enough groans to get their attention. "Looks like someone woke up," the female said. He heard footsteps approaching. _LIGHT!_ It was blinding at first. John blinked a few times to let his eyes adjust. He didn't waste this chance; he knew the possibility of them blindfolding him again was high. He took a glance at all of them. He was right about one thing, the two males were vorcha. The female though… it shocked him… a quarian? _Why is a quarian helping the vorcha attack a human colony?_ John wondered. She bent down next to him. "Don't worry, we don't bite," she said as she removed the gag. "Speak, tell us everything about you." Before the quarian could bring her hand back to her side, John gave her a nasty bite on the hand. She screamed in sudden shock. The tow vorcha drew their weapons but the quarian stopped them. "No! Don't kill him, he could be valuable!"

"Screw that, he is a waste of life!" the third vorcha yelled. John's eyes looked over to see the vorcha's weapon about to fire at him. He pulled the quarian's hand violently with his mouth, forcing her on top of him. _Just in time!_ John thought. BANG! The quarian fell dead on top of him. He acted fast. Turning sideways slightly to use the quarian's knife on her belt to cut him free. He got up to see both vorcha aiming at him. Before they could shoot he lifted the quarian's lifeless body and used it as a shield. "Where is my sister?" John asked.

"Human, thinking you could get away from us!?" one of them yelled.

"No, as long as my sister does I don't care what happens to me," he replied with confidence in his voice.

"You die here and now!" Before he could fire he suddenly dropped dead from a bullet to his head. The second vorcha turned rapidly to see nothing but a bullet headed straight for him. Dead. They were both dead from an unknown soldier. John dropped the body and ran towards the soldier. "Help you have to help me find my sister!" he yelled, tears swelling in his eyes. The soldier removed the helmet they wore. It was his mom. "Mom! They took Elli…" before he could continue he was cut off by her.

"I know…" she said as her head lowered. John studied her. She had red eyes, ones that showed she had cried. "John…" she said as her voice became weaker.

"What's wrong? What happened?!" John asked beginning to panic.

"Your sister…" her voice gave in and tears began to fall. "I'm so sorry John…." John was speechless. He had nothing to say. "I thought Eden Prime would be safe… I… I thought wrong…" Tears were now flowing freely down her face. She was looking at the ground, unable to see John's sorrowful eyes.

"We will make it though this though right?" John asked quietly.

"I don't know," she said.

"We will…" John said no ounce of fear in his voice. "You know why?"

His mom looked up at his confident eyes. "Because we are Shapards… and a Shepard can do anything if they have the will…" She said, regaining her composure. The two embraced. They didn't know it would be the last time….

* * *

The next year, John ran away. He didn't only run, he smuggled his way across the universe. In his heart he knew he could never see his father or mother again, he had failed them. He failed Elli. He traveled everywhere. To all the home worlds. Sur'Kesh… Palavan… Tuchunka… and the one that stuck out was the Migrant Fleet. Otherwise known as the Quarian Flotilla.

He didn't know how but he was aloud to enter. Not a lot of outsiders are aloud to enter the Migrant Fleet. _How come they let a runaway sixteen year old intro the fleet but not top ranking military officers?_ John wondered. The ship was amazing. He asked the quarian guards escorting him everything, from the type of engines they use right down the ventilation system. Even though he had to wear a rebreather helmet, he still asked questions regarding the vents. As they walked down the hall he noticed the very different colors of the suites they wore. All of them were ranging from every color. He also noticed they all had the same skin color. Even with the suites, he could see through enough to see the eye and skin color. A purple, not bright or dark, just purple. Most had bright pink or bright purple eyes. Though there were those few with blue. He was presented to the admiralty board, the head admirals of the fleet. He told them that he was training for the Alliance N7 program. He explained how he was able to track them down, they were in the outer rim, the most unexplored and uninhabited system in the entire galaxy. Few people even knew it existed. He then told them that in order to join, you need to have knowledge of all the races. They were reluctant at first but they quickly realized that anyone who was able to track down the vast but hidden Migrant Fleet was worthy of such information. They told him everything, their entire history leading all the way up to the fall of Rannoch to the geth. "Do geth…." before John could finish his question, a quarian in a purple and black environment suit walked in. John and the five admirals turned their heads to the quarian.

"Sorry admirals, but… did… did I interrupt something important?" the quarian asked nervously.

"Please, calm down Tali," Koris informed her. "This is John Shepard, he is here on business for the Alliance."

"Oh...I… I am deeply sorry to intrude…" Tali stumbled.

Shepard gave out a small chuckle. "Quiet alright miss…?"

"Tali'Zorah nar Rayya, pleased to meet you," she told him as they shook hands.

"What is it you require Tali?" Raan asked.

"Well… I was just wondering…" Tali's fingers were tingling together, she was nervous. "My pilgrimage…" she finally said.

"Ah yes…" Koris said. "Well no ships are currently available at the moment…" he informed her, looking at his omni tool.

"She can come with me," John informed them. The admirals were in shock, but only for a second before they all exchanged nods.

"Very well, what is your ship name?"

"The SSV Organ admiral."

"Commander John Shepard vas Organ, you have our permitting to take Tali'Zorah vas Organ, IF she chooses to accept." Raan said turning her attention to Tali.

Tali was in deep thought for a minute. _Wait for another month or two for another one to return from their pilgrimage or go with this stranger I never met before… He is alliance and he trying for N7. He must be good right? _"I accept."

"Then, Tali'Zorah vas Organ, travel with your new captain, and come home reborn!" Koris announced.

"I will bring her back safely admirals." John informed them. He turned to face her. Their eyes meeting, "I promise."

* * *

The shuttle was small. Smaller then most at least. John and Tali were on there way back to the Organ. "So tell me about yourself," John asked politely.

"Not much to know," Tali said with a small chuckle. "I'm a quarian. I've spent my whole life on the Rayya."

"That doesn't matter," John told her with a serious but humorous tone, "I spent my whole life living alone, doesn't mean I don't got a story!"

"Well now," Tali said, growing nervous, "I suppose..." Tali began to run her fingers together. John took a mental note of it. _So I know how to tell when shes nervous, that should help in the future... I hope..._ Shepard thought.

"There's no need to be nervous Tali, your among a friend," John assured her.

_A human that respects quarians? I don't understand._ "That... that is... very new to me," Tali admitted.

"I know, quarians don't usually get respect. But I for one think they deserve it due to their knowledge of technology," he told her with a reassuring smile.

"My people... I don't know why... why do we always get the crap end of things? What did we do..." Tali's voice became saddened as her head lowered.

John moved to sit next to her. He took his hand and gently lifted it up. "You, Tali'Zorah, did nothing. Your people did nothing. They just happened to do the right thing at the wrong time."

She smiled, which John could see through the mask. "I think you are a very good at convincing people," Tali said with a wide smile and small laugh.

"I think you know when the truth is spoken," he replied, also with a smile.

* * *

**AN: Ok so I would spend some time behind everything leading up to ME but I am just going to cover the events right before the Normandy and all that. Once again, this is a AU so just bare with me LUL**

* * *

**Two Years Later...**

"Normandy huh..." Tali mumbled to John, who was standing at the docking bay window, looking down at the SSV Normand SR1. It was a new prototype ship the turians helped commission.

"Yea, we will be under the command of Captain David Anderson."

"I read his file, he is a good guy," Tali said, trying to convince John the new ship would be good for him.

"So have I Tali, he just seems..." John struggled to find the word, "Strict."

"Well yea, he is the commander of one of the most advanced ships in the Alliance AND Citadel space," Tali said.

"I don't know. It just doesn't seem like it would fit my tactics."

"Tactics?" Tali laughed for a minute. John looked at her with a face of disappointment "Your definition of tactics is running into a suicide mission and risking everyone's lives every chance you get," Tali said, still laughing.

"Yea, yea, yea..." John replied, knowing he lost the battle. "I guess we better report in..." he said with a grumble.

"Come on you little brat," Tali replied.

"Shut up _mom_," John replied wide smiled. Tali just shook her head in laughter and the two were off to start their new adventures on the Normandy.


	2. Return to Eden Prime

**Wow, I didn't think I would get some good praise for that first chapter. I only got one review but got several likes and fallows, which made me very very happy.**

**Roronoa Star96: Thank you very much for that. Hope you enjoy!**

**Every one else who liked/fallowed: Thank you all, I hope you enjoy the AU I have come up with.**

**UPDATE: I will be posting polls with the chapters. The polls will help me decide the events of the story. Of course I will have the final say, but I want your opinion on what you want to see. A example of a poll might be, Who should survive Virmire? A. Ashley or B. Kaiden. Stuff like that. The first poll has been posted on my page. You will have one week after each poll is posted to vote before the next one is up.**

* * *

**Chapter 2  
Return to Eden Prime**

* * *

The Normandy was small. One of the crewmen, Jenkins, took John and Tali on a tour which only lasted half an hour. John was impressed with the ship but Tali… After only a few seconds after setting foot on it, she whispered to John "_This is our new home_."

"And here is the engine room," Jenkins told them as he stopped in front of the large engine.

Tali was in awe. _How could such a powerful ship be powered by that small engine? And it's so quiet…_ She wondered. She stepped in before Jenkins could speak again, "Do you mind if I stay down here? I love the engine room already!" Tali exclaimed excitedly.

"Of course Miss Zorah, I'll let Adams know when I see him," Jenkins said as he showed her over to a couple of computers. "This is the main workstation; of course you do have to go into the vents occasionally." Jenkins informed her.

"Oh don't worry about me," Tali said sarcastically as she turned to John, "I've lived _my whole life_ on a ship," she said, referring to the first day the two met. John laughed while Jenkins looked confused trying to figure out what they did.

"Don't worry Jenkins, it's an old joke between us," John said, patting the young soldier on his back. Jenkins gave out a chuckle. The intercom then struck on, "Jenkins, bring the commander to the comm room for a briefing," said a voice. It was low but it had a good man behind it. John knew it must be the captain.

"Right away sir," Jenkins replied with a stern tone. "Commander," Jenkins said as he shifted to the door. John nodded and fallowed him to the comm room, leaving Tali in her dream world.

Jenkins left John to find his way due to reasons unknown. John did notice him eyeing the med bay on the way; he assumed he was trying to get doctors permission to go on an upcoming mission. John chuckled at the thought, a _fully trained marine has to ask permission to go on a simple mission._ Before they boarded, John and Tali had been told they were going to accomplice the crew on a simple pickup on Eden Prime.

When John entered the comm room, he was surprised to see a turian in red clad armor and not a human. "Captain Anderson?"

"Ah, Commander Shepard, I was hoping you would arrive first," the turian said in his raspy voice, one that resembled most turians. "I'm Nihlus Kryik, I am a Spectre for the Citadel Council," he said officially.

"I didn't think they would send a Spectre for such a simple mission," John replied. _There has to be more going on here_, John thought to himself.

"They don't," said a deep voice from behind. John turned to see a darker skinned man approaching. "I'm captain David Anderson, I've read a lot about you commander," Anderson stated as he reached to shake his hand. John also reached for a handshake.

As they shook, John spoke up, "Then what's the real mission sir?"

"We found something that may help every race in citadel space," Nihlus said. John glanced at him with both a curious and nervous face. "A team on Eden Prime uncovered a beacon of some sort. It's prothean." He said, voice dying down at the last word.

"Prothean?" John replied. He knew about the protheans. That they built the mass relays, and were an advanced space faring race before they mysteriously disappeared fifty thousand years ago. "I thought they were extinct."

"They are, but the technology they left behind is still useful. This could launch humanity farther another thousand years!" Anderson exclaimed.

"Indeed, I needed to see this for myself," Nihlus said.

"That's not all you're here for though," John said aloud. He bit his tongue. _Fuck, why did you say that out loud!?_

"I guess your file was correct then, you can truly sense someone," Nihlus said.

"Nihlus is here to evaluate you," Anderson said. "You've been nominated to become a Spectre."

"What… me…" John was in shock. _Who would nominate me?_

"Yes, I had to see your skills for my own," Nihlus informed him.

"Who… who would nominate me…." John muttered.

"Your young friend Tali'Zorah," Anderson replied.

John was once again taken off guard. "She seemed highly confident that you could accomplish this task," Anderson continued, "I believe in you too. To be the first human Spectre will show the other species just how far we've come,"

"I'm sure most of them will except you into our ranks," Nihlus jumped in. _He just said **most** of them._

"What do you mean most of them?" John asked.

"The only two who appose are Turian Senator, Frytill and the Batarian Senator Oleg. They both respect humans, but they don't think they are ready for such a large role."

Before anyone else could speak a voice came over the intercom. "Captain, incoming transmission from Eden Prime sir!"

"Put it on screen Joker," Anderson commanded. On screen, a group of soldiers appeared. They were all firing at an unknown enemy, at least unknown to them due to the camera angle. A soldier in front of the camera was suddenly dragged away by some humanoid figure. Shepard was beginning to think it was another slave attack, like the one from his childhood. A female soldier in pink and white armor ran up and yelled for the camera man to get down. The men were suddenly wide eyed and looking towards the sky. The camera finally reached where their eyes were aimed only to meet a giant hand like ship. One that was massive in size. Bigger then the Destiny Ascension, the largest ship in all citadel space. After a few more seconds it cut to static. The man on the intercom came back, "No comm traffic at all sir, it just dies," he said nervously.

"Well… looks like things just got a little more complicated," John said.

"You leave in ten, report to the cargo bay once you're ready," Anderson said walking away, leaving Nihlus and Shepard alone again.

"What do you think it is?" John asked.

"I honestly don't know," Nihlus replied, "Guess we'll find out."

Nihlus left and John was alone. "And into the inevitable we go…"

* * *

Tali was sitting at her new work space in the engine room. Although a few of the other crewmen didn't like Tali or quarians in general, but Adams thought she would be the most helpful crewmen on the whole ship. John walked in quietly. He searched around for a moment and spotted Tali working on a pipe that lead to the drive core. John approached, Tali heard his heavy boots against the metal floor in the room. "Hey John," she started as she turned to face him, "What's up, how'd the meeting with the captain go?"

"Good," John started casually, "unless you find out you got nominated for something that is considered impossible among humans," he said sarcastically.

"Wait… they… they told you about…. the Spectre nomination?"

"Yea, they have a Spectre named Nihlus who will be evaluating me," John informed her.

"Look, I wanted to tell you…"

"Tali why would you nominate me?" John asked, "You know that if I became a Spectre then we would be split apart," John said with sadness.

"I didn't want to tell you till I was off…" Tali started, voice getting weak. "I am going back to the fleet…"

"Tali…" John started, eyes begging to swell, "Why didn't you tell me you were leaving?"

"I didn't want to upset you," she replied. Her voice was getting weaker. John could see a slight sparkle starting beneath her eyes. John could tell she was crying.

With his hand in a fist, he slowly lifter her downed head for their eyes to meet. "I've known you for two years," John started, "You have been one of my longest and my closest friends. I understand if you have to leave," John said, holding back his tears.

For a moment, there was silence. Nothing but the two hugging in a embrace. Once they broke apart, John spoke up, "When do you leave?"

Tali once again lowered her head. Only for a moment, however, then she looked back up to him. "I leave after the Eden Prime mission," she said. John nodded his head. It was his turn to look down. "I'm sorry," Tali added.

"Don't be," he said as he looked back up and faked a smile.

"I know you're upset. I can tell," she said in a humored tone, trying to cheer him up.

John gave out a small smile, "You know me to well."

"I know…"

* * *

She was running. Running faster than any human could. Her breathing was heavy. _I am not going to die here_, her mind screamed. Bullets hit the ground near her feet. She pulled out her pistol, still running fast. She dove to the ground in front of her and spun around. _Shot Shot Shot_. The three geth turrets that fallowed her were now in pieces on the floor.

IN the distance she could see two geth shock troopers with a human civilian. She leaned forward slightly to get a better look. They lifted him atop some sort of tripod. Suddenly, a large spike shot up through his chest, lifting him up into the air and his body sliding down about halfway. She noticed sparks of electricity shocking around his center. _How did the geth get this kind of tech?_, she wondered. One of the troopers looked in her direction she quickly spun around and ran for a nearby rock. She sat with her back against, trying to gain composure and some breath. She turned to see the two geth approaching. She readied her weapon. As she turned to fire on them, they burst into flames. One had its head blown off while the other bleed the white synthetic blood and slowly died.

She turned to see... _a turian? What the hell is a turian doing here?_

Behind him approached two humans. One was roughly 6'3 with short black hair. The other was a tall 6'8 and had short blonde hair. The turian was in red clad armor and had white face paint. The tallest human approached her. "You ok soldier?" he asked with compassion in his eyes.

"I... I.. um.." her voice as subtle and calm but still had distress in it. John grabbed her shoulder as she began to drift away. He lifted her up and studied her.

"You might be going into shock," he informed her, "just breath nice and slow, everything will be ok," he assured her.

She did as he said. "I... I think I'm ok."

"Whats your name soldier," the turian asked.

"Ashley. Ashley Williams. Gunnery Chief."

"Hi Ashley, I'm Commander John Shepard," John said, "this is Kaiden Alenko and council Spectre Nihlus Kryik."

"Thank you for saving me," Ashley said as she slowly got to her feet. She was wearing normal marine armor that was mainly white with a pink trimming.

"Where are here to get the prothean beacon, do you know where it is?" Nihlus asked.

"It was at the dig site, just up ahead."

Shepard then turned to the two men, "Nihlus take point, Alenko cover the left flank while I get the right," he commanded.

Before anyone could fallow through, Ashley spoke up. "I wanna go with you."

Nihlus and Kaiden exchanged looks of disapproval, but of course it wasn't up to them, it was up to Shepard. "Are you able to fight?" he asked.

"Ready to get some payback sir!" she yelled.

John shook his head, "I don't like it when soldiers fight to get payback, it could result in the death of people around you."

"Of course sir," Ashley replied, "I can fight."

"Alright then, cover the rear," John said as he began to walk forward, weapon drawn again.

"Sir!" Ashley replied as she fell back.

* * *

The rest of the mission was relatively quiet. Until they reached the spaceport. They found the body of a marine. Ashley identified him as her squads commander. A human, who was hiding behind some crates, said the attacker was a Spectre named Saren. Nihlus expressed his feelings about Saren and about how Saren hates humanity. They were told that he took the beacon to the other end of the station. They fallowed.

* * *

As they stepped off the tram, Ashley pointed out a bomb. "Shit, they are trying to cover up the whole thing!" Kaiden yelled to the commander.

"Can you disarm it?" He quickly replied.

"I can," Ashley said.

"Do it!"

"Shep, we got company!" Nihlus yelled as a squad of geth shock and rocket troopers emerged from the nearby corner.

"Ash, disarm it, everyone move to cover her!"

After disarming all the bombs they easily took out the remaining geth. After searching for several minutes, they found the beacon. "Normandy come in, we have the beacon." Shepard said over the comm link.

The beacon was emitting a strange mist that alerted Ashley. She approached. "It wasn't doing that when we found it," she mumbled to herself. She was suddenly being dragged towards it, like a force was pushing her. John saw her over the shoulders of Nihlus and Kaiden. He took of running. He jumped up and grabbed her out of the air. He wasted no time; he violently threw her out of the way, only for himself to be picked up. Ashley tried to save him but Kaiden and Nihlus stopped her.

Shepard was getting a vision. _SYNTHETICS... DEATH... FIRE... DEATH... WAR... DEATH..._

The beacon suddenly exploded and John flew backwards, unconscious. The three scrambled and tried to revive him. It was useless, he was knocked out cold.

* * *

**Hope you enjoyed this short chapter. Sorry, Eden Prime was always a long boring mission for me. I hope you like the whole Nihlus surviving thing. I also noticed my Shepard has no description as to what he looks like besides eye color (bright green) and height (6'8). So here is a description.  
He has the same hair as Kaiden but his color is more of a bright brown almost blonde. He has the same skin tone as the default Male Shep. His armor is the normal N7 but the coloring is different The main color is black. The secondary is yellow. The pattern is pattern #2 (from ME2 and ME3) and the color of it is also yellow. The backlight is yellow. Ok. That's it. REVIEW!**


	3. Don't Say Good-Bye

**Ok so the chapters (until Mass Effect 2) will be relatively short mainly because the first ME had missions that could take two and a half hours and I don't like writing out stuff like that so until ME2, the chapters will have only 1000-2000 words. After ME, the chapters will be around 4000-5000 words. Also, make sure to vote on the new poll on my page. I will have a new poll up with each chapter. It will let me see what you guys think should happen during major events (an example being, Save Ashley or Kaiden. So basically the major events.)**

**Para-Cord: I did get inspiration from him. We discussed it and we are heading in completely different directions so no need to worry. Regardless, I think he is doing way better then me. I recommend you fallow his story as well.  
**

**WojoClan: I understand you liking my story, but I don't like when people say "Oh your story is way better then his" I would like to hear stuff like predictions, suggestions, and how I could improve. I don't want to hear that I'm better then someone else. I like everyone to get credit for their own work and believe that it is unethical for someone to say something like that. Please keep reading and reviewing but no more of that. PS- I am part Russian comrade ;-)**

**Roronoa Star96: Yes but you this is an AU, you never know what can happen ;-)**

**TW6464: Yes. Nihlus will play a much bigger part, not only in ME but in ME2 and ME3.**

* * *

**Chapter 3  
Don't Say Good-bye**

* * *

_What the hell. Where am I?_, John thought to himself. It was a planet. It had plants everywhere. It reminded John of Eden Prime. But there was something... _different. What's that?_, John asked himself as a tall humanoid approached. It walked through him, as if he was a ghost. Suddenly there was a flash, the planet was now in flames. IN the sky a huge synthetic that looked similar to a squid, it was firing a red beam that was destroying everything in its path. The humanoid creatures were fighting back. They were giving it all, yet, it had no affect on the creature. Then, the beam shot down near his position. _LIGHT_. There was nothing now. Just darkness.

* * *

John was lying in the medic bay. He was unconscious for two hours. Two hours of nothing. Just silence. Then again... he was a Shepard... A woke up with a big gasp of air. Everyone in the room was startled by his sudden revival. Tali was the first to say anything. "Doctor Chakwas, he's waking up!"

John tried to sit up but instantly laid back down due to a sharp pain to his head. He started to blink rapidly, trying to focus his vision. He couldn't though. It was if something wanted him to go back to sleep. "What... what's happening to him?" Tali asked in a worried voice.

"Seizure!" Chakwas replied as she grabbed a syringe. She walked over and jabbed it into his chest, near the heart and lungs. After several seconds, John went limb. "He should return to normal in..." Before she could finish John woke up. Heavy breathing fallowed.

His vision was finally focused enough to see Tali, Chakwas, Nihlus, and Ashley surrounding him. "What the hell," he muttered. He then found him self around Tali's arms.

"Don't ever scare me like that again!"

John gave out a small chuckle, "Yea, ok _mom_." Tali let go and laughed. Nihlus then approached.

"Good to see you alive Shepard. Ashley, Kaiden, and I dragged you back of the beacon exploded. You've been here for two hours," Nihlus explained.

"Thanks," John said looking at Nihlus and then at Ashley, who was sitting on the other bed comfortably.

"That's what we have to do when a fellow soldier is down," Ashley replied.

Chakwas cut in, "Well besides some off the scale brain activity, you're completely unharmed. I believe the cap..." She was cut off as Anderson walked in.

"Doctor," he started with politeness in his voice, "Hows our new XO holding up?"

"I feel great," John said with a fake cough, "Never better."

Tali shook her head with a laugh, "He's fine captain."

"Good, now if excuse, Nihlus, Shepard, and I have something to talk about," Anderson announced.

"No problem," Tali said turning to John, "If you need me, I'll be in engineering."

John nodded. Ashley, Chakwas, and Tali all left the room, leaving the three men to themselves. "Nihlus told me what happened, and about Saren," Anderson said.

"Well, shouldn't we talk to the council or something?" John asked.

"Indeed we should," Nihlus said, "We are on our way to the Citadel right now. Me being a Spectre should help the council see Saren's treachery."

"Our ETA is one hour, until then you have some free time. I recommend reading Saren's profile, if you need access to classified information Nihlus can help you," Anderson said.

"Sir," Shepard replied with a salute. The three of them walked out and left their separate ways.

* * *

"You feeling alright?" Tali asked as John walked into engineering.

"Yea, a little dazed still but I'll be fine."

"Good, I'd hate to see my only friend die because he did a stupid stunt," she said sarcastically, "I mean really, if anything you should die a hero's death."

"Geez, thanks."

"No problem."

"So are you getting a ride from the Citadel back to the fleet?"

Tali looked down for a moment and returned to his gaze. "No. I'm not leaving."

"What? Why?" John asked.

"I can't leave you. You mean to much to me," Tali stated.

John showed a face of confusion. "You are the only human I have ever known that looks at quarians as another species and not a disgraceful race. You have been kind to not only me, but every quarian. Remember when we were aboard the Organ, and we had to rescue the crew of that damaged ship. There were quarians on-board that the captain said to leave behind. Instead you saved them, and sacrificed several squad mates to make sure they survived. Maybe to your people you are a disgrace for doing that. But I... I think it is the most noble thing someone can do."

John was just starring. He was in awe. That the shy quarian girl he met two years ago was as motivational and skilled in speech as he was. "Don't just stare at me. John, your family to me. I can't leave you," Tali said as she lifted her hand up to his cheek.

John reached up and pressed it against his face. "I know. I can't let you leave either," John said with a smile. The two hugged in a loving embrace. As they separated, John spoke, "I..." before he could finish Joker came over the intercom.

"You're needed on the bridge commander"

"On my way," John said as he left. _I wonder what he was going to say?_

* * *

**Ok so I pumped this chapter out fast but as I stated, most of the ME1 chapters will be short. Sorry about that. I just think the more in depth stuff starts in ME2 and continues into ME3. ME1 is more like a setting up the story type thing. Anyways, REVIEW!**


	4. AU Note: READ FOR NEWS

**Ok just wanted to say this (Even though we are not aloud to have AU but whatever)**

**This is being written by me (Cody) and my best friend/life long friend (Bella) make sure to keep that in mind.**

**Bella is the one who writes the chapters (aside from the AU at the beginning and end of each chapter).**

**I am the one who writes out the overall story and all that. I write a basic overview of the chapter, then she turns it into what you read. I am also the one who writes all the dialogue, character stories, main story, side plots, and all that.**

**I want to say this so you give credit to both of us.**

**The only other thing, we both have school and (since we are at a tech school) we have advanced projects. We are currently working on one right now so be ready for long waits when it comes to when chapters are released.**

**That is all we have to say.**

**Bella: Thank you for reading this.**

**Cody: It means alot.**


	5. Taking Command

**UPDATE 4/14/13: I am taking a break but if you wanna see what I'm up to check out my profile.**

**Ok, chapter 4! Yay! Not much to say except the fact that my OC will be introduced! And the first decision, which is based on my poll and chosen by you, will also be revealed in this chapter!**

**WojoClan: Hahaha, make it easy, why in this great galaxy would I do that? IF anything, this is when it really gets difficult. I am planning on breaking Shepard down to his core. Imagine (SPOILER) how 117 and all the halo fans felt when Cortana died, yea imagine that times fifty. That's how much pain I will cause Shepard, Tali, Liara, Garrus, Kasumi, and all the other beloved ME characters will feel. I did say it is dark and gritty, and by god I meant it!**

**Ok so that response (the one from WojoClan) is a HUGE sneak peek, or sort-of-sneak-peak. This is not the normal universe. This will quickly turn into a tear jerker for fans of the series and more specificly its characters. So if you think that your favorite characters suffering is sad, get ready to cry your eyes out! MWHAHAHAHAHAH**

**_Disclaimer: I do not own any of the characters or storylines from Mass Effect, Mass Effect 2, or Mass Effect 3 and all the DLC. I only own the upcoming OC that will appear. Everything else belongs to the brilliant minds at Bioware._  
**

**Bella: Yea, Cody aint kidding when it comes to crying. I cried alot while writting these chapters.**

**Cody: Oh yea, she's helping to. Just to let you all know, I write the story/plotlines while Bella... writes the story. Yea... Hope that makes sense**

**Bella: Of course it does.**

**Cody: Alright, on with the...**

**Bella: I wanna say it for once! ON WITH THE SHOW!**

* * *

**Chapter 4  
****Taking Command**

* * *

"What's up. I don't think we've met yet," John said as he approached the pilots seat of the Normandy.

"Hey, I'm Jeff, but you can call me Joker," the pilot replied.

"You needed me..."

"Yea. I think I deserve to meet the new XO of my baby," Joker replied with a chuckle.

"I see you like the Normandy."

"Like?" Joker asked in a humorous voice, "The Normandy is my ship. I can't get a girl with my brittle bones, but this will do."

"What to do you mean, brittle bones?"

"I have Vrolik syndrome. It makes my bones as brittle as toothpicks," Joker explained.

"Well for someone like that, you sure have done good to come this far," Shepard said with a respectful tone.

"Damn commander, that quarian was right about you."

"Who... Tali?"

"Yea, Tali."

"When did you two talk?"

"When you were brought aboard from Eden Prime," Joker started, "She went on and on how you are one of the most noble, polite, and intriguing humans she ever met."

"Intriguing?"

"Yea. She was talking about how you are completely different then other humans. Your..." Joker searched for the word, "... John Shepard."

"Hmm... I'll take it," Shepard replied with a laugh.

Outside the porthole was a large space station. It had five long arms. On the arms was lights. It was a city. The arms extended to a circular middle that had a large tower.

Shepard was just starring. For someone who had never been to the citadel, it was a normal reaction. Nihlus, who was walking up form behind, gave out a chuckle. "Amazing... isn't she?" he asked the stunned commander.

"Amazing...? She's indescribable," Shepard replied.

Tali the entered. "Wow, the Citadel. I never thought I would ever come here."

"Me either," Shepard replied.

"Really? You're a N7 soldier and candidate for the Spectres, you didn't think you wouldn't come here?" Joker asked.

"Well before that yea."

"It doesn't matter now, you're here," Nihlus replied.

"What the hell is that ship?! That big one there!" Tali was yelling in both fear and excitement.

"That's the Destiny Ascension, the largest ship in the entire fleet," Nihlus replied.

"Size isn't everything, I could outrun it," Joker replied.

"We should still be thankful it's on our side," Shepard said.

"I would love to see that engine room," Tali mumbled.

* * *

The Citadel tower was tall. John was amazed, as was Tali. The two asked Nihlus and Anderson every possible question regarding the Citadel.

As they entered the Citadel tower, they saw a two turians. One was in c-sec armor while the other was in an advanced red turian armor. "I know I can get the evidence, I just need access to his Spectre files and I can stop him!" yelled the c-sec officer.

"I'm sorry Vakarian, but that's off limits," the other replied, "Just give up, you can't prove anything. This will only result in humiliation for you!"

The c-sec officer shook his head. The turian in the red walked away irritated John approached the stranded c-sec officer. "Commander John Shepard," the officer announced, "Garrus Vakarian, c-sec officer," he said has he extended to shake John's hand.

As they shook John spoke, "Am I really that well known?"

Garrus gave out a small laugh, "Yea, everyone knows the legend of the great Jennifer Shepard. Her son is making a name for himself as well."

"I guess so." Garrus shifted slightly as Nihlus and Tali approached. "This is Tali and Nihlus, there here to help me in the trial."

"Yea, I tried to find some evidence to help, isn't working out to well. That bastard has all his stuff locked up. Not even the council can have it unless he says so," Garrus replied with defeat filling his voice.

"Maybe this will help," John replied. He reached into his utility belt and pulled out a data-pad As he handed it to Garrus, Nihlus stepped forward. "Shepard, what are you doing? You can't give him those files!" Nihlus whispered in his ear.

"These files should help you," John told Garrus, completely disregarding Nihlus's comment on the matter.

Garrus became wide eyed, "How did..."

"Luck," John said as he walked away.

* * *

As they walked up the steps, they saw Anderson. "Come on, the meeting already started," he said in a rush.

After several minutes of Udina and the council debating, the asari councilor, Tela Vasir. spoke up. "Enough! This arguing is nothing more then a waste of time!"

"These humans have no evidence to support their claim!" The turian councilor, Frtyill Melsark, snapped.

"I agree, they have no proof of Saren's involvement," the batarian councilor, Oleg Qshy, replied.

"They also have a Spectre on their side," the salarian councilor, Jaeto Verata, said trying to convince them.

"All of you silence!" the asari councilor yelled. "We haven't let Shepard or Nihlus explain their side of the story," she said, her voice back to its calm state.

"Fine, let Nihlus speak first," Frtyill said almost in a yell.

Nihlus stepped forward. "My councilors, I know of Saren's hate for humanity," he started; "He has spoken to me on several occasions about the presence of humans. He always spoke of them as a lesser race that would accomplish nothing. I used to think that. Till I met John Shepard. After this one mission with him, I can say that he has sparked something within my heart. His compassion shows that not all humans are filled with hate. I know see that Saren was not speaking jokingly. He was telling the truth. With eye witness testimony and my own personal stories, this should be all the proof you need."

"What say you Shepard?" Oleg asked curiously.

Nihlus backed down and John stepped up. He took a slow deep breath, but made it unnoticeable by anyone. "Councilors, I don't have anything to tell you besides what I know and saw," John started; "Based on all the files, along with Nihlus's and the witness's accounts, everything points to Saren. The fact is that Saren despises humanity You know it's true. I think he is planning something else however. Something that will threaten everyone and everything. I had a vision. I received it from the prothean beacon. I saw death... destruction... and I also saw synthetics. That would explain the geth's involvement. I hope this is all the proof you need," John finished.

The four councilors exchanged looks. "If there is no other evidence," Tela started but was interrupted.

"Here it is!" Garrus yelled as he ran up to the stand, "Here is the evidence!"

"Who is this? He is not apart of this trial!" Oleg yelled.

"My name is Garrus Vakarian, c-sec vet, I found evidence against Saren!"

"What is it then?" Jaeto asked in his quick salarian accent.

"It's a tape. I found it thanks to the help of a quarian. She was on something called a pilgrimage Anyways, she was working with the Shadow Broker, but she was set up. Saren set her up! I was able to recover this tape from her before she died," Garrus announced.

"Play the tape," Frtyill demanded in a quiet tone.

As the tape played, only one thing stuck out in John's mind. _Reaper_.

"This evidence is irrefutable," Jaeto said.

"Thank you, all of you, for bringing this to light," Oleg said.

"Indeed, you may have saved alot of lives," Frtyill added.

"I hate to skip the celebrations but there still is the matter of capturing him," Nihlus said.

"Yes, his Spectre status will be stripped and we will have c-sec look into the situation," Tela announced.

"That's it?" John asked in almost a yell. _Fuck! You have to learn to shut your mouth!_

"Well now, if Saren is working with the geth and trying to get away from us, then he will most likely go to the Terminus system," Oleg explained, "Like you know, we cannot enter."

"Maybe we you can't but..." Nihlus started. "You know it's the right choice!"

Frtyill and Oleg shook their heads. "Commander John Shepard of the SSV Normandy SR1, step forward," Tela said.

_Oh my... this is really happening! I'm becoming a Spectre!_

John's memory flashed back to his mom.

"Please state your full name," Oleg informed him.

John was snapped back to reality. "John James Shepard."

"Please kneel," Jaeto asked. John did so.

Oleg spoke first: "Spectres is the first line of defense of the Council, it's armed arm."

Tela fallowed: "Spectres operate beyond the law, beyond jurisdiction, beyond morals."

Frtyill was third: "They do what must be done, so others don't have to."

Jaeto was last: "A Spectre is an ideal."

"A shadow meant to light up the darkness."

"A savior whose deeds will go unsung."

"Commander Shepard, arise a Spectre," Tela said with joy but subtlety.

"Commander Shepard, arise a Spectre," Jaeto said with hope.

"Commander Shepard, arise a Spectre," Oleg said with some regret.

"Commander Shepard, arise a Spectre," Frtyill said with a monotone voice.

John let go of his breath. He held it in since they asked him to kneel. He was greeted by a hug from Tali as he stood.

"Thanks," John said as they departed.

"Right, your going to need a ship, crew, funding. Anderson and I will arrange all this. Be in the docking bay in one hour," Udina said as they all walked away from the council and back down to the elevator.

* * *

Tali, Garrus, and Nihlus all congratulated John on his achievement. As John stood looking out over the Citadel presidium, Nihlus walked up. "Well this is farewell Commander."

"What? Why?"

"I may be able to accompany you but I have my own mission to attend to. Besides, my place is here," Nihlus stated.

"It's up to you, but if you ever need anything," John extended his hand and the two shook, "You can always count on me."

"Thanks, I better be off." With at, Nihlus left while Tali and Garrus approached.

"Well if it isn't the first human Spectre, COMMANDER JOHN SHEPARD!" Garrus yelled.

John shook his head in laughter. "I'm proud of you," Tali said.

"Thanks..."

"Well as much as I love to stick around, I must be off. Duty calls for a c-sec officer," Garrus said with sadness. As he walked away he heard John yell something. He ignored him.

"HEY VAKARIAN!"

He couldn't help but turn.

"Get your ass over here and help me stop this bastard!" John yelled.

Garrus laughed, as did Tali and John. When he was back in front of them he spoke up, "You really need a sniper and assault expert that's been with c-sec for more than five years?"

"Five? I thought it was eight?" John asked with a smile.

"I'm not that old," Garrus replied.

"Yea, what are you like eighty?"

"Ha ha ha, very funny. I'm twenty four," Garrus stated, "In human years of course," he quickly added.

"Enough of age, you wanna join my crew or what?"

"Two words Shepard. Hell. Yes."

* * *

As they approached the elevator to the docking bay, they were stopped by a krogan. He was large, like most, but looked more fierce. A large scar on his face really made them nervous as to what he wanted. "You John Shepard?" he asked in a deep voice.

"Yea, and you are?" John asked.

"Wrex. Urdnot Wrex."

"You need something?"

"Yes, I wanna help you take down Saren," he stated. John was suddenly interested.

"What do you have against Saren?" he asked.

"He sent geth scout teams to Tuchunka, I want them out! I will reunite the krogan clans but the geth are threatening that."

"What's your skill set?"

"He's krogan, I say we keep him," Garrus said.

"Alright fine, but any sign of violence towards the crew and your gone," John stated.

* * *

"Captain Anderson has stepped down as commanding officer, the ship if yours now," Udina said.

John was shocked. He was a captain of a ship. He thought of his mom again but snapped himself back. "Any leads on Saren?"

"Yes, we have reports of geth on several planets. The ones that stick out would be Noveria and Feros. We also have reports of them on Omega."

"Omega? Why would they go there?" Garrus asked.

"We don't know, I would check it out first," Anderson suggested.

"We also suggest you find Doctor Liara T'soni, an expert on the protheans She went missing somewhere in the Hades Gamma. If you find her, she could be of great use."

"Alright, he'll head to Omega first," John told his squad.

"Good luck Shepard." Udina said as he walked off.

John walked towards Anderson. "Thanks, this means alot," he said.

Anderson just smiled. "Careful, she just got a new paint job."

* * *

**Hope you enjoyed. OC will appear next chapter. So the first decision made by you guys was Omega as the starting point. Which means either Feros or Noveria will not occur (since you only need the three locations to finish the game). Other than that: REVIEW!**

**UPDATE: POLL IS UP! VOTE NOW!**


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